def add_most_severe_consequence(
tc: hl.expr.StructExpression) -> hl.expr.StructExpression:
"""
Add most_severe_consequence annotation to transcript consequences
This is for a given transcript, as there are often multiple annotations for a single transcript:
e.g. splice_region_variant&intron_variant -> splice_region_variant
"""
return tc.annotate(most_severe_consequence=csqs.find(
lambda c: tc.consequence_terms.contains(c)))
def add_most_severe_consequence_to_consequence_minus_splice(
tc: hl.expr.StructExpression) -> hl.expr.StructExpression:
"""
Copied from gnomad_hail but slight change
"""
csqs = hl.literal(all_coding_minus_splice)
return tc.annotate(most_severe_consequence=csqs.find(
lambda c: tc.consequence_terms.contains(c)))
def split_info_annotation(
info_expr: hl.expr.StructExpression, a_index: hl.expr.Int32Expression
) -> hl.expr.StructExpression:
"""
Splits multi-allelic allele-specific info fields.
:param info_expr: Field containing info struct.
:param a_index: Allele index. Output by hl.split_multi or hl.split_multi_hts.
:return: Info struct with split annotations.
"""
# Index AS annotations
info_expr = info_expr.annotate(
**{
f: info_expr[f][a_index - 1]
for f in info_expr
if f.startswith("AC") or (f.startswith("AS_") and not f == "AS_SB_TABLE")
},
AS_SB_TABLE=info_expr.AS_SB_TABLE[0].extend(info_expr.AS_SB_TABLE[a_index]),
)
return info_expr